PLUMED-NEST

Project ID: plumID:23.044
Source: plumed_files/plumed.dat
Originally used with PLUMED version: 2.5
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

Click on the labels of the actions for more information on what each action computes

fullThe GROUP action with label full calculates the following quantities:
 Quantity   
 Type   
 Description  
full
atoms
indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1-60
cppThe GROUP action with label cpp calculates the following quantities:
 Quantity   
 Type   
 Description  
cpp
atoms
indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=198-297
c1The COORDINATION action with label c1 calculates the following quantities:
 Quantity   
 Type   
 Description  
c1
scalar
the value of the coordination: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=full GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=cpp R_0The r_0 parameter of the switching function=0.25 
c1: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=full GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=cpp R_0The r_0 parameter of the switching function=0.25  D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0
METADUsed to performed metadynamics on one or more collective variables. More details ...
 LABELa label for the action so that its output can be referenced in the input to other actions=metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential
metad.acc
scalar
the metadynamics acceleration factor
 ARGthe labels of the scalars on which the bias will act=c1
 HEIGHTthe heights of the Gaussian hills=2
 PACEthe frequency for hill addition=20000
 SIGMAthe widths of the Gaussian hills=0.5
 BIASFACTORuse well tempered metadynamics and use this bias factor=20
 GRID_MINthe lower bounds for the grid=0
 GRID_MAXthe upper bounds for the grid=100
 GRID_BINthe number of bins for the grid=400
 FILE a file in which the list of added hills is stored=HILLS
 ACCELERATION Set to TRUE if you want to compute the metadynamics acceleration factor
... METAD

COMMITTORDoes a committor analysis. More details ...
  ARGthe labels of the values which is being used to define the committor surface=c1
  STRIDE the frequency with which the CVs are analyzed=500
  BASIN_LL1List of lower limits for basin #=-0.1
  BASIN_UL1List of upper limits for basin #=0.1
... COMMITTOR

The COMMITTOR action with label  calculates somethingPRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=c1,metad.* FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=500